1Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.

Abstract

High-throughput techniques for detecting DNA polymorphisms generally do not identify changes in which the genomic position of a sequence, but not its copy number, varies among individuals. To explore such balanced structural polymorphisms, we used array-based Comparative Genomic Hybridization (aCGH) to conduct a genome-wide screen for single-copy genomic segments that occupy different genomic positions in the standard laboratory strain of Saccharomyces cerevisiae (S90) and a polymorphic wild isolate (Y101) through analysis of six tetrads from a cross of these two strains. Paired-end high-throughput sequencing of Y101 validated four of the predicted rearrangements. The transposed segments contained one to four annotated genes each, yet crosses between S90 and Y101 yielded mostly viable tetrads. The longest segment comprised 13.5 kb near the telomere of chromosome XV in the S288C reference strain and Southern blotting confirmed its predicted location on chromosome IX in Y101. Interestingly, inter-locus crossover events between copies of this segment occurred at a detectable rate. The presence of low-copy repetitive sequences at the junctions of this segment suggests that it may have arisen through ectopic recombination. Our methodology and findings provide a starting point for exploring the origins, phenotypic consequences, and evolutionary fate of this largely unexplored form of genomic polymorphism.

In this example, two haploid parental strains harbor a particular genomic region (black) on different chromosomes. Crossing the parents leads to a diploid that contains two copies of the transposed segment. Sporulation leads to either a tetratype (TT) pattern (one duplication and one deletion); a non-parental ditype (NPD) pattern (two duplications and two deletions), or a parental ditype (PD) pattern (neither duplications nor deletions). The relative frequencies depend on the position of the transposed segment relative to the centromeres in each parent.

(A) aCGH data for all tetrads across chromosome XV. The area within the red box contains TS15.1, and is shown in more detail in panel B, (B) Raw aCGH data and (C) inferred duplications (yellow) and deletions (blue).

Based on the aCGH data, deletion of TS15.1 was expected in spore 27A. Probes tested in all six tetrads are indicated by asterisks. Due to the repetitive nature of subtelomeric segments 0–10, PCR assays produced ambiguous results (marked as “not determined”). See also .

Model for the position and structure of TS15.1 in the parental strains.

Boxes represent annotated genes (tall) and intergenic regions (short). Systematic gene names for probe numbers are given in . (A) Chromosome XV of S288C. Probes are color-coded as being either outside the transposed region (green), within the transposed region (pink), or as containing an endpoint (yellow). (B) Chromosome IX of S288C. The TS breakpoint is indicated by an asterisk. (C) The inferred position and orientation of the TS is shown for Y101 using the color scheme from panel A. The shading in panels B and C shows the cosegregation pattern of Y101 chromosome IX probes with those on S288C chromosome XV according to the GMS data. (D) Genotyping results for the chromosome IX segment in tetrad 55, showing evidence of recombination between YIL158W and YIL157C.

Experimental validation of the transposition of TS15.1 in strain Y101.

(A) Ethidium bromide stained chromosomes of S288C, S90, and Y101 separated by pulsed field gel electrophoresis. (B) A Southern blot using YOL158C (from within TS15.1) as hybridization probe. In Y101, the probe hybridizes to chromosome IX but not chromosome XV. Note that 3 pairs of chromosomes cannot be distinguished on the gel, including chromosomes XV and VII.

Comparative genomic evidence that S288C harbors the ancestral form of TS15.1.

Annotated genes (open boxed arrows) are shown for S. paradoxus and S. bayanus contigs relative to the known structure of the region in S288C and the inferred structure in Y101. S. paradoxus contig 539 matches the gene order of S288C across the proximal endpoint of TS15.1 while S. bayanus contig 223 matches the gene order of S288C across the distal endpoint. The green bar shows the position of the gap on chromosome XV of Y101. Each scalebar tick represents 1 kilobase.